def reload_lme4(self, install=False):
"""Reload information about lme4, optionally installing it"""
# set the binary
binary = self.lme4_rpath.text()
if pathlib.Path(binary).is_file():
try:
rsetup.set_r_path(binary)
except RUnavailableError as exc:
QtWidgets.QMessageBox.information(
self, "No compatible R version found",
"The R/lme4 functionality is not available.\n\n" +
f"{exc.__class__.__name__}: {exc}")
# check lme4 package status
if not rsetup.has_r():
r_version = "unknown"
lme4_st = "unknown"
else:
r_version = rsetup.get_r_version()
if rsetup.has_lme4():
lme4_st = "installed"
else:
lme4_st = "not installed"
if install and lme4_st == "not installed":
self.setEnabled(False)
rsetup.install_lme4()
self.setEnabled(True)
# update interface with installed lme4
self.reload_lme4(install=False)
else:
# update user interface
self.pushButton_lme4_install.setVisible(lme4_st == "not installed")
self.label_r_version.setText(r_version)
self.label_lme4_installed.setText(lme4_st)
def reload_lme4(self, install=False):
"""Reload information about lme4, optionally installing it"""
# set the binary
binary = self.lme4_rpath.text()
if pathlib.Path(binary).is_file():
rsetup.set_r_path(binary)
# check lme4 package status
if not rsetup.has_r():
r_version = "unknown"
lme4_st = "unknown"
else:
r_version = rsetup.get_r_version()
if rsetup.has_lme4():
lme4_st = "installed"
else:
lme4_st = "not installed"
if install and lme4_st == "not installed":
self.setEnabled(False)
rsetup.install_lme4()
self.setEnabled(True)
# update interface with installed lme4
self.reload_lme4(install=False)
else:
# update user interface
self.pushButton_lme4_install.setVisible(lme4_st == "not installed")
self.label_r_version.setText(r_version)
self.label_lme4_installed.setText(lme4_st)
def __init__(self, parent, *args, **kwargs):
QtWidgets.QWidget.__init__(self, parent=parent, *args, **kwargs)
path_ui = pkg_resources.resource_filename("shapeout2.gui",
"preferences.ui")
uic.loadUi(path_ui, self)
self.settings = QtCore.QSettings()
self.parent = parent
# Get default R path
if RPY2_AVAILABLE and rsetup.has_r():
rdefault = rsetup.get_r_path()
else:
rdefault = ""
# disable R settings
self.tab_r.setEnabled(RPY2_AVAILABLE)
#: configuration keys, corresponding widgets, and defaults
self.config_pairs = [
["advanced/developer mode", self.advanced_developer_mode, "0"],
["check for updates", self.general_check_for_updates, "1"],
["dcor/api key", self.dcor_api_key, ""],
["dcor/servers", self.dcor_servers, ["dcor.mpl.mpg.de"]],
["dcor/use ssl", self.dcor_use_ssl, "1"],
["lme4/r path", self.lme4_rpath, rdefault],
]
# extensions
store_path = os_path.join(
QStandardPaths.writableLocation(QStandardPaths.AppDataLocation),
"extensions")
self.extensions = ExtensionManager(store_path)
self.reload()
# signals
self.btn_apply = self.buttonBox.button(
QtWidgets.QDialogButtonBox.Apply)
self.btn_apply.clicked.connect(self.on_settings_apply)
self.btn_cancel = self.buttonBox.button(
QtWidgets.QDialogButtonBox.Cancel)
self.btn_ok = self.buttonBox.button(QtWidgets.QDialogButtonBox.Ok)
self.btn_ok.clicked.connect(self.on_settings_apply)
self.btn_restore = self.buttonBox.button(
QtWidgets.QDialogButtonBox.RestoreDefaults)
self.btn_restore.clicked.connect(self.on_settings_restore)
# extension buttons
self.checkBox_ext_enabled.clicked.connect(self.on_ext_enabled)
self.pushButton_ext_load.clicked.connect(self.on_ext_load)
self.pushButton_ext_remove.clicked.connect(self.on_ext_remove)
self.listWidget_ext.currentRowChanged.connect(self.on_ext_selected)
self.listWidget_ext.itemChanged.connect(self.on_ext_modified)
# lme4 buttons
self.pushButton_lme4_install.clicked.connect(self.on_lme4_install)
self.pushButton_lme4_search.clicked.connect(self.on_lme4_search_r)
# tab changed
self.tabWidget.currentChanged.connect(self.on_tab_changed)
def on_action_compute_significance(self):
# check that R is available
if rsetup.has_r():
dlg = compute.ComputeSignificance(self, pipeline=self.pipeline)
dlg.exec()
else:
QtWidgets.QMessageBox.critical(
self, "R not found!",
"The R executable was not found by rpy2. Please add it " +
"to the PATH variable or define it manually in the " +
"Shape-Out preferences.")
def __init__(self, parent, *args, **kwargs):
QtWidgets.QWidget.__init__(self, parent=parent, *args, **kwargs)
path_ui = pkg_resources.resource_filename("shapeout2.gui",
"preferences.ui")
uic.loadUi(path_ui, self)
self.settings = QtCore.QSettings()
self.parent = parent
# Get default R path
if RPY2_AVAILABLE and rsetup.has_r():
rdefault = rsetup.get_r_path()
else:
rdefault = ""
# disable R settings
self.tab_r.setEnabled(RPY2_AVAILABLE)
#: configuration keys, corresponding widgets, and defaults
self.config_pairs = [
["advanced/developer mode", self.advanced_developer_mode, 0],
[
"advanced/check pyqtgraph version",
self.advanced_check_pyqtgraph_version, 1
],
["check for updates", self.general_check_for_updates, 1],
["dcor/api key", self.dcor_api_key, ""],
["dcor/servers", self.dcor_servers, ["dcor.mpl.mpg.de"]],
["dcor/use ssl", self.dcor_use_ssl, 1],
["lme4/r path", self.lme4_rpath, rdefault],
]
self.reload()
# signals
btn_apply = self.buttonBox.button(QtWidgets.QDialogButtonBox.Apply)
btn_apply.clicked.connect(self.on_apply)
btn_ok = self.buttonBox.button(QtWidgets.QDialogButtonBox.Ok)
btn_ok.clicked.connect(self.on_apply)
btn_restore = self.buttonBox.button(
QtWidgets.QDialogButtonBox.RestoreDefaults)
btn_restore.clicked.connect(self.on_restore)
# lme4 buttons
self.pushButton_lme4_install.clicked.connect(self.on_lme4_install)
self.pushButton_lme4_search.clicked.connect(self.on_lme4_search_r)
def test_basic_setup():
assert rsetup.has_r()
rsetup.install_lme4()
assert rsetup.has_lme4()